BTEP maintains several Question and Answer Forums of interest to the NCI/CCR community.
Currently, there are forums on these topics listed below:
If you wish to ask a question go to the Ask Question Page and submit your question.
Droplet-based (e.g. 10x Genomics) or plated-based (e.g. Smart-Seq)? When should one be considered over the other
What is the difference between high throughput single cell methods like droplet-barcoding (like 10x Genomics Chromium) and plate-based methods (ike 'Smart-Seq")? Which is more sensitive? What is the comparative cost of each?
1 Answer:
A key difference between Smart -Seq2 and the 10x Chromium protocol lies in the way the RNA is processed to cDNA. Smart-seq2 captures the full-length mRNA, although with significant 3′ bias because of oligo dT primers used during cDNA generation, while the 10x protocol is based on a 3′-tag sequencing method Accordingly, it is important to consider the aim of the study when selecting a method for single-cell RNA-seq. For example, full-length capture is needed for studies concerned with isoforms or gene fusions, while 3′-tag methods can capture more cells and thus give an aggregate view of the transcriptional heterogeneity of a given cell population. https://doi.org/10.1093/bfgp/elx035
Answered on July 29th, 2020 by kimia.dadkhah@nih.gov